tbuckley/cabot-search huggingface dataset:
Abstract 4038: Study of therapeutic effects of polyisoprenylated cysteinyl amide inhibitors on lung cancer cells of black patients using 3D-Printed alveolar model
Authors: Nadine Belony, Bing Ren, Phuc Pham, Matthew Gregory, Pablo E. Puente, Nazarius S. Lamango, Ite A. Offringa, Yong Huang
Journal: Cancer Research (2022)

Abstract Lung cancer is one of the top five deadliest cancers, and black Americans have a higher mortality rate when compared to white Americans even though they smoke relatively fewer cigarettes. Lung adenocarcinoma (LUAD) is the most common histological lung cancer subtype in all population groups including blacks. There are no in vitro model systems to study lung cancer in black subjects, and there is only one lung adenocarcinoma cell line from a black patient (NCI-H23). Here we aim to address the lack of in vitro models to study black LUAD. Using three-dimensional (3D) biofabrication technologies, we’ve developed a thick vascularized tissue model to recapitulate physiologically relevant heterogeneous human alveoli. Specifically, the blood-air barrier of the alveolar model is simulated with two perfusable channels embedded in a thick vascularized tissue construct: a helical blood channel and a straight air channel. Spatially, the air channel is in the center and is surrounded by the blood channel. Human endothelial cells are seeded onto the inner surface of the blood channel and NCI-H23 cells (which carry a KRAS mutation) or untransformed alveolar epithelial cells derived from black subjects, are seeded on the inner surface of the air channel. The blood and air channels are perfused using cell medium and oxygenated air, respectively. The model is used for the study of potential LUAD therapeutic agents such as polyisoprenylated cysteinyl amide inhibitors (PCAIs), which target and disrupt the RAS-mediated signaling pathway. KRAS is the most commonly mutated oncogene in LUAD in blacks, and our experiments are aimed at ensuring that PCAIs are effective in black LUAD and may offer better treatment outcomes for ethnically/racially diverse patients in whom the RAS signaling pathway is frequently altered and for whom pharmaceutical therapy is necessitated by the late diagnoses. Citation Format: Nadine Belony, Bing Ren, Phuc Pham, Matthew Gregory, Pablo E. Puente, Nazarius S. Lamango, Ite A. Offringa, Yong Huang. Study of therapeutic effects of polyisoprenylated cysteinyl amide inhibitors on lung cancer cells of black patients using 3D-Printed alveolar model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4038.
Updated Efficacy Outcomes of Anti-PD-1 Antibodies plus Multikinase Inhibitors for Patients with Advanced Gastric Cancer with or without Liver Metastases in Clinical Trials
Authors: Hiroki Yukami, Akihito Kawazoe, Yi-Tzu Lin, Shohei Koyama, Shota Fukuoka, Hiroki Hara, Naoki Takahashi, Takashi Kojima, Masako Asayama, Takako Yoshii, Hideaki Bando, Daisuke Kotani, Yoshiaki Nakamura, Yasutoshi Kuboki, Saori Mishima, Masashi Wakabayashi, Takeshi Kuwata, Masahiro Goto, Kazuhide Higuchi, Takayuki Yoshino, Toshihiko Doi, Hiroyoshi Nishikawa, Kohei Shitara
Journal: Clinical Cancer Research (2022)

Abstract Purpose: We previously reported preliminary activity of regorafenib plus nivolumab (REGONIVO) or lenvatinib plus pembrolizumab (LENPEM) in advanced gastric cancer (AGC). Meanwhile, several studies demonstrated liver metastases are less responsive to immunotherapy. Patients and Methods: Combined efficacy outcomes with a longer follow-up in a phase Ib trial of REGONIVO and a phase II trial of LENPEM were examined in AGC with or without liver metastases (REGONIVO plus LENPEM cohort). We also investigated the efficacy of anti-PD-1 monotherapies (anti-PD-1 monotherapy cohort). A comparison of the immune microenvironment between gastric primary tumors and liver metastases was also conducted by multiplex IHC. Results: In the REGONIVO plus LENPEM cohort, with a median follow-up of 14.0 months, objective response rate (ORR), median progression-free survival (mPFS), and median overall survival (mOS) were 46%, 7.8 months, and 15.6 months in patients with liver metastases, while 69%, 6.9 months, and 15.5 months in those without. In the anti-PD-1 monotherapy cohort, with a median follow-up of 27.6 months, ORR, mPFS, and mOS were 9%, 1.4 months, and 6.4 months in patients with liver metastases, while 22%, 2.3 months, and 9.0 months in those without. Multiplex IHC revealed liver metastases were associated with an abundance of immune-suppressive cells, such as tumor-associated macrophages and regulatory T cells, with fewer CD8+ T cells compared with gastric primary tumors. Conclusions: Anti-PD-1 antibodies plus regorafenib or lenvatinib for AGC showed promising antitumor activity with a longer follow-up, irrespective of liver metastases status, despite a more immune-suppressive tumor microenvironment in liver metastases.
Polarization-Sensitive Endobronchial Optical Coherence Tomography for Microscopic Imaging of Fibrosis in Interstitial Lung Disease
Authors: Sreyankar Nandy, Sarita R. Berigei, Colleen M. Keyes, Ashok Muniappan, Hugh G. Auchincloss, Michael Lanuti, Benjamin W. Roop, Angela R. Shih, Thomas V. Colby, Benjamin D. Medoff, Melissa J. Suter, Martin Villiger, Lida P. Hariri
Journal: American Journal of Respiratory and Critical Care Medicine (2022)

"Polarization-Sensitive Endobronchial Optical Coherence Tomography for Microscopic Imaging of Fibrosis in Interstitial Lung Disease." American Journal of Respiratory and Critical Care Medicine, 206(7), pp. 905–910
Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses
Authors: Chuanyi Zhang, Palash Sashittal, Michael Xiang, Yichi Zhang, Ayesha Kazi, Mohammed El-Kebir
Journal: Molecular Biology and Evolution (2022)

Abstract Transcription regulatory sequences (TRSs), which occur upstream of structural and accessory genes as well as the 5′ end of a coronavirus genome, play a critical role in discontinuous transcription in coronaviruses. We introduce two problems collectively aimed at identifying these regulatory sequences as well as their associated genes. First, we formulate the TRS Identification problem of identifying TRS sites in a coronavirus genome sequence with prescribed gene locations. We introduce CORSID-A, an algorithm that solves this problem to optimality in polynomial time. We demonstrate that CORSID-A outperforms existing motif-based methods in identifying TRS sites in coronaviruses. Second, we demonstrate for the first time how TRS sites can be leveraged to identify gene locations in the coronavirus genome. To that end, we formulate the TRS and Gene Identification problem of simultaneously identifying TRS sites and gene locations in unannotated coronavirus genomes. We introduce CORSID to solve this problem, which includes a web-based visualization tool to explore the space of near-optimal solutions. We show that CORSID outperforms state-of-the-art gene finding methods in coronavirus genomes. Furthermore, we demonstrate that CORSID enables de novo identification of TRS sites and genes in previously unannotated coronavirus genomes. CORSID is the first method to perform accurate and simultaneous identification of TRS sites and genes in coronavirus genomes without the use of any prior information.
Effectiveness of TNF-inhibitors, abatacept, IL6-inhibitors and JAK-inhibitors in 31 846 patients with rheumatoid arthritis in 19 registers from the ‘JAK-pot’ collaboration
Authors: Kim Lauper, Michele Iudici, Denis Mongin, Sytske Anne Bergstra, Denis Choquette, Catalin Codreanu, René Cordtz, Diederik De Cock, Lene Dreyer, Ori Elkayam, Ellen-Margrethe Hauge, Doreen Huschek, Kimme L Hyrich, Florenzo Iannone, Nevsun Inanc, Lianne Kearsley-Fleet, Eirik Klami Kristianslund, Tore K Kvien, Burkhard F Leeb, Galina Lukina, Dan C Nordström, Karel Pavelka, Manuel Pombo-Suarez, Ziga Rotar, Maria Jose Santos, Anja Strangfeld, Patrick Verschueren, Delphine Sophie Courvoisier, Axel Finckh
Journal: Annals of the Rheumatic Diseases (2022)

Background JAK-inhibitors (JAKi), recently approved in rheumatoid arthritis (RA), have changed the landscape of treatment choices. We aimed to compare the effectiveness of four current second-line therapies of RA with different modes of action, since JAKi approval, in an international collaboration of 19 registers. Methods In this observational cohort study, patients initiating tumour necrosis factor inhibitors (TNFi), interleukin-6 inhibitors (IL-6i), abatacept (ABA) or JAKi were included. We compared the effectiveness of these treatments in terms of drug discontinuation and Clinical Disease Activity Index (CDAI) response rates at 1 year. Analyses were adjusted for patient, disease and treatment characteristics, including lines of therapy and accounted for competing risk. Results We included 31 846 treatment courses: 17 522 TNFi, 2775 ABA, 3863 IL-6i and 7686 JAKi. Adjusted analyses of overall discontinuation were similar across all treatments. The main single reason of stopping treatment was ineffectiveness. Compared with TNFi, JAKi were less often discontinued for ineffectiveness (adjusted HR (aHR) 0.75, 95% CI 0.67 to 0.83), as was IL-6i (aHR 0.76, 95% CI 0.67 to 0.85) and more often for adverse events (aHR 1.16, 95% CI 1.03 to 1.33). Adjusted CDAI response rates at 1 year were similar between TNFi, JAKi and IL-6i and slightly lower for ABA. Conclusion The adjusted overall drug discontinuation and 1 year response rates of JAKi and IL-6i were similar to those observed with TNFi. Compared with TNFi, JAKi were more often discontinued for adverse events and less for ineffectiveness, as were IL-6i.
Duplication of <i>NRAMP3</i> Gene in Poplars Generated Two Homologous Transporters with Distinct Functions
Authors: Mathieu Pottier, Van Anh Le Thi, Catherine Primard-Brisset, Jessica Marion, Michele Wolf Bianchi, Cindy Victor, Annabelle Déjardin, Gilles Pilate, Sébastien Thomine
Journal: Molecular Biology and Evolution (2022)

Transition metals are essential for a wealth of metabolic reactions, but their concentrations need to be tightly controlled across cells and cell compartments, as metal excess or imbalance has deleterious effects. Metal homeostasis is achieved by a combination of metal transport across membranes and metal binding to a variety of molecules. Gene duplication is a key process in evolution, as emergence of advantageous mutations on one of the copies can confer a new function. Here, we report that the poplar genome contains two paralogues encoding NRAMP3 metal transporters localized in tandem. All Populus species analyzed had two copies of NRAMP3, whereas only one could be identified in Salix species indicating that duplication occurred when the two genera separated. Both copies are under purifying selection and encode functional transporters, as shown by expression in the yeast heterologous expression system. However, genetic complementation revealed that only one of the paralogues has retained the original function in release of metals stored in the vacuole previously characterized in A. thaliana. Confocal imaging showed that the other copy has acquired a distinct localization to the Trans Golgi Network (TGN). Expression in poplar suggested that the copy of NRAMP3 localized on the TGN has a novel function in the control of cell-to-cell transport of manganese. This work provides a clear case of neo-functionalization through change in the subcellular localization of a metal transporter as well as evidence for the involvement of the secretory pathway in cell-to-cell transport of manganese.
Abstract 1305: Tumor Treating Fields (TTFields) promote a pro-inflammatory phenotype in macrophages
Authors: Yiftah Barsheshet, Boris Brant, Tali Voloshin, Alexandra Volodin, Lilach Koren, Bella Koltun, Anat Klein-Goldberg, Efrat Zemer-Tov, Tal Kan, Rom Paz, Moshe Giladi, Uri Weinberg, Yoram Palti
Journal: Cancer Research (2022)

Abstract Introduction: Tumor Treating Fields (TTFields) are low intensity (1-3 V/cm), intermediate frequency (100-500 kHz), alternating electric fields that are delivered non-invasively to tumors. TTFields therapy is approved in the US and Europe for the treatment of patients with glioblastoma or mesothelioma. In addition to an established anti-mitotic mechanism of action, previous studies have shown that TTFields-induced cell death stimulates anti-tumor immunity and promotes the maturation of dendritic cells. In the current research, the effect of TTFields on the polarization of unstimulated macrophages and the phenotypic regulation of M1 and M2 macrophages was investigated. Methods: Bone marrow-derived macrophages (BMDMs) were generated from the femurs and tibias of 5-8-week-old Balb\C mice. TTFields (150 kHz) were applied for 24 h to unstimulated (M0 phenotype) BMDMs and BMDMs stimulated with LPS+IFN-γ (M1 polarization) or IL-4 (M2 polarization). Flow cytometry was used to identify surface expression of the macrophage biomarker F4/80 and activation markers CD80, major histocompatibility complex class II (MHC II), inducible nitric oxide synthase (iNOS), CD206, and ARG-1. Multiplexed secretion assays were conducted to quantify CXCL1 (KC), IL-18, IL-23, IL-12p70, IL6, TNF-α, IL-12p40, free active TGF-β1, CCL22 (MDC), IL-10, IL-6, G-CSF, CCL17 (TARC), and IL-1β as to examine the heterogeneity of the stimulated macrophages. Results: The percentage of cells expressing the pro-inflammatory M1 markers CD80+ and MHC IIhigh was significantly increased following application of TTFields to polarized (M1 or M2) or unpolarized BMDMs, while expression of the M2 markers CD206 and ARG-1 was significantly decreased. A pro-inflammatory secretion pattern, with increased levels of CXCL1, IL-18, IL-23, IL-12p70, TNF-α, IL-12p40, CCL22, G-CSF, CCL17 and IL-1β was observed in cell supernatants of M1 and M2 stimulated BMDMs, and unstimulated M0 BMDMs, following delivery of TTFields. Taken together, TTFields polarized unstimulated BMDMs to the M1 phenotype, and induced phenotype skewing of M2 polarized BMDMs to the M1 phenotype. Conclusions: TTFields therapy displays a novel immunoregulatory role in macrophage polarization and promotes a pro-inflammatory phenotype. Future investigations will focus on defining the underlying mechanism of this phenotypic skewing. Citation Format: Yiftah Barsheshet, Boris Brant, Tali Voloshin, Alexandra Volodin, Lilach Koren, Bella Koltun, Anat Klein-Goldberg, Efrat Zemer-Tov, Tal Kan, Rom Paz, Moshe Giladi, Uri Weinberg, Yoram Palti. Tumor Treating Fields (TTFields) promote a pro-inflammatory phenotype in macrophages [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1305.
Abstract 2125: Towards a spatial view of immune cell function in cancer
Authors: Maryam Pourmaleki, Caitlin J. Jones, Brian D. Greenstein, Sabrina D. Mellinghoff, Daniel A. Navarrete, Smrutiben A. Mehta, Nicholas D. Socci, Ingo K. Mellinghoff, Travis J. Hollmann
Journal: Cancer Research (2022)

Abstract Immunotherapy can result in lasting tumor regressions, but despite its success, only a subset of patients and cancer types benefit from immunotherapy. Thus, uncovering features of the tumor microenvironment (TME) that contribute to this differential response can inform candidates for novel therapies and biomarkers for patient stratification. Recent advances in single-cell technologies allow for profiling of cell states and their spatial interactions within a tumor. Here, we performed multiplexed immunofluorescence (mpIF), a method for in situ single-cell measurement of 30+ proteins, as well as bulk transcriptomics and genomics on 180 tumor samples across 4 immunotherapy-responsive and -resistant solid and liquid cancers: in-transit melanoma (ITM), non-small cell lung cancer (NSCLC), glioblastoma multiforme (GBM), and classical Hodgkin lymphoma (cHL). In aggregate, we measured over 100 million single cells and identified over 1,000 unique tumor and immune cell states. We uncovered immune-suppressive cell states, such as macrophages negative for PD-L1 and B7-H3 in immunotherapy-resistant ITM tumors and all GBM tumors, which generally fail to respond to immunotherapy. In GBM, macrophages exhibited two distinct spatial topologies, infiltrated or excluded. In ITM, we identified pre-treatment cell states and gene expression signatures that associate with immunotherapy response such as MHC class I expression on the tumor cell surface, B cell aggregates, “exhausted” PD-1/LAG-3/TIM-3 triple-positive CD8+ T cells, and expression of interferon-gamma genes. We observed a similar immune checkpoint-rich (PD-1/LAG-3/TIM-3 triple-positive) TME in all cHL tumors, which have remarkably high immunotherapy response rates. We spatially defined the microniche (30-micron radius neighborhood) of “exhausted” CD8+ T cells, and within the microniches, found antigen presentation competent tumor cells, proliferating T cells, and B7-H3 positive macrophages, which together contribute to an activated TME. Together, we present a statistical workflow for the integrated analysis of spatially resolved multidimensional data for cancer target discovery that is tailored towards application in routinely collected formalin-fixed paraffin-embedded cancer biospecimens. Citation Format: Maryam Pourmaleki, Caitlin J. Jones, Brian D. Greenstein, Sabrina D. Mellinghoff, Daniel A. Navarrete, Smrutiben A. Mehta, Nicholas D. Socci, Ingo K. Mellinghoff, Travis J. Hollmann. Towards a spatial view of immune cell function in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2125.
Comparison of Screening Colonoscopy Rates After Positive Noninvasive Testing for Colorectal Cancer in States With and Without Cost-Sharing
Authors: Douglas Barthold, Kai Yeung, David Lieberman, A. Mark Fendrick
Journal: JAMA Network Open (2022)

This cohort study examines the colorectal cancer (CRC) screening rates in 2 US states that have implemented policies to eliminate consumer cost-sharing of CRC screening and compares these rates with those of neighboring states that have not enacted similar policies.
Abstract 5077: Proteomics analysis of extracellular vesicles from pancreatic cancer cells and cancer associated fibroblasts
Authors: Sharon Pan, Lisa A. Lai, Diane M. Simeone, David W. Dawson, Yuanqing Yan, Tatjana Crnogorac-Jurcevic, Ru Chen, Teresa A. Brentnall
Journal: Cancer Research (2022)

Abstract Extracellular vesicles (EVs) are comprised of lipid bound vesicles secreted by cells into the extracellular environment with various roles in cell-to-cell communication. Recent studies have implicated EVs in cell proliferation, epithelial-mesenchymal transition (EMT), metastasis, angiogenesis, and mediating the interaction of tumor cells and tumor microenvironment. To systematically characterize the EVs associated with pancreatic cancer, we performed proteomic and functional analyses on the protein contents of EVs released from pancreatic cancer lines, CAF cell lines and a normal pancreatic epithelial cell line. More than 1400 non-redundant proteins were identified in each EV proteome derived from these cell lines. The common EV proteins identified in these cell lines were enriched in biological processes such as vesicle-mediated transport and exocytosis. Protein networks relevant to pancreatic tumorigenesis, such as of EMT, complement and coagulation components, were significantly enriched in the EVs from cancer cells or CAFs in comparison to normal pancreatic epithelial cells. These findings support the roles of EVs as a potential mediator in transmitting EMT signals and complement response in the tumor microenvironment and possibly contributing to coagulation defects related to cancer development. Citation Format: Sharon Pan, Lisa A. Lai, Diane M. Simeone, David W. Dawson, Yuanqing Yan, Tatjana Crnogorac-Jurcevic, Ru Chen, Teresa A. Brentnall. Proteomics analysis of extracellular vesicles from pancreatic cancer cells and cancer associated fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5077.
Correspondence on “PICaSSO Histologic Remission Index (PHRI) in ulcerative colitis: development of a novel simplified histological score for monitoring mucosal healing and predicting clinical outcomes and its applicability in an artificial intelligence system” by Gui<i>et al</i>
Authors: Emily C L Wong, Parambir S Dulai, Neeraj Narula
Journal: Gut (2022)

<h3>ABSTRACT</h3> Cancer rates vary widely across vertebrate groups. Identifying species with lower-than-expected cancer prevalence can help establish new models for unraveling the biological mechanisms underlying cancer resistance. Theoretical predictions suggest that cancer prevalence should be positively associated with body mass and longevity in animals. Yet, in mammals, the best studied vertebrates in terms of cancer, this prediction does not hold true: a phenomenon known as Peto’s paradox. Despite mounting work disentangling the biological basis of Peto’s paradox, it is still relatively unknown whether other major vertebrate groups behave similarly to mammals or might hold new keys to understanding cancer biology. Here, we present the largest dataset available so far on cancer prevalence across all major groups of tetrapod vertebrates: amphibians, birds, crocodilians, mammals, squamates (lizards and snakes), and turtles. We investigated cancer prevalence within and among these groups and its relationship with body mass and lifespan. This is the first study to analyze non-avian reptile groups separately. We found remarkably low cancer prevalence in birds, crocodilians, and turtles. Counter to previous studies, we found that body mass and lifespan are inversely related to cancer prevalence in mammals, although Peto’s paradox still holds true in this group. Conversely, we rejected Peto’s paradox in birds and squamates, as neoplasia prevalence was positively associated with body mass in these groups. The exceptionally low cancer prevalence in turtles and extensive variation in cancer prevalence amongst vertebrate families hold particular promise for identifying species with novel mechanisms of cancer resistance.